[AMBER] Combined cartesian and NMR restraints

From: Parker de Waal <Parker.deWaal.vai.org>
Date: Fri, 26 Sep 2014 01:43:54 +0000

Hello Everyone,

After reading through some of the old mailing list threads regarding the various workarounds for ntr =1 and nmropt=1, I still need some clarification.

I have an NVT prod.in as show below:

NVT prod
 &cntrl
  irest=1, ntx =5,
  nstlim=5000000, dt=0.002,
  ntpr=500, ntwr=500, ntwx=500,
  temp0=300.0,
  ntt=3, gamma_ln=5, ntb=1, ntp=0,
  ntc=2, ntf=2, ig=-1,
  cut=9,
  ioutfm = 1,
  iwrap=1, nmropt=1,
  ntr=1,
 &end
 &wt type='END' /
DISANG=rst.dist

Now I wish to add cartesian restraints, following the snippet here: http://ambermd.org/Questions/constraints.html into my rst.dist file as seen below:

# N373 D69 VS
 &rst
  ixpk= 0, nxpk= 0, iat= 5235, 6651, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
      rk2=0.0, rk3=25.0, ir6=1, ialtd=0,
 &end
... (lines removed)
# A150 F244 VS
 &rst
  ixpk= 0, nxpk= 0, iat= 2310, 9472, r1= 0.00, r2= 0.00, r3= 6, r4= 7,
 &end
Hold GPCR fixed
20.0
RES 1 708
END
END

However whenever I run this the follow error occurs:

   5. REFERENCE ATOM COORDINATES

  default_name
    ----- READING GROUP 1; TITLE:
 DISANG=rst.dist

     rfree: End of file on unit 5

If someone could provide some input on how to achieve this I would greatly appreciate it.

Best,
Parker
 

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Received on Thu Sep 25 2014 - 19:00:02 PDT
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